The phenotype of an individual organism is either its total physical appearance and constitution or a specific manifestation of a trait, such as size, eye color, or behavior that varies between individuals. Phenotype is determined to some extent by genotype, or by the identity of the alleles that an individual carries at one or more positions on the chromosomes. Many phenotypes are determined by multiple genes and influenced by environmental factors. Thus, the identity of one or a few known alleles does not always enable prediction of the phenotype.

Nevertheless, because phenotypes are much easier to observe than genotypes (it doesn't take chemistry or sequencing to determine a person's eye color), classical genetics uses phenotypes to deduce the functions of genes. Breeding experiments can then check these inferences. In this way, early geneticists were able to trace inheritance patterns without any knowledge of molecular biology.

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. The fitness of an organism is a high-level phenotype determined by the contributions of thousands of more specific phenotypes. Without phenotypic variation, individual organisms would all have the same fitness, and changes in phenotypic frequency would proceed without any selection (randomly).

The interaction between genotype and phenotype has often been conceptualized by the following relationship:

genotype + environment → phenotype

A slightly more nuanced version of the relationships is:

genotype + environment + random-variation → phenotype

An example of the importance of random variation in phenotypic expression is Drosophila flies in which number of eyes may vary (randomly) between left and right sides in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.

According to the autopoietic notion of living systems by Humberto Maturana, the phenotype is epigenetically being constructed throughout ontogeny, and we as observers do the distinctions that define any particular trait at any particular state of the organism's life cycle.